I've generated an editor for my metamodel with Eugenia and now I'm trying to find a way to execute a manually written code inserted in the automatic generated java implementation of "op1". I marked the implementation of "op1" as "generated NOT" and added a dummy, for example, system.out.println("anything"). How can I call the method "op1" while I'm running the generated GMF Editor?

You'll need to define an extension to the org.eclipse.ui.popupMenus extension point to do this. http://www.ibm.com/developerworks/opensource/tutorials/os-eclplgns/section4.html provides a good tutorial on this. You'll need to set objectClass to org.eclipse.gmf.runtime.diagram.ui.editparts.IGraphicalEditPart instead of org.eclipse.core.resources.IFile, and then you can access the underlying EObject using resolveSemanticElement().

Your suggestion seems to be very helpfull. But, I would like to know
whether there is any way to do this without creating a new plugin. Is it
possible to change one of the eclipse projects generated automatically by
EuGENia from the metamodel (showed below) to achieve this?

For example, eugenia generate a interface ClTest.java and an implementation
ClTestImpl.java for the class ClTest. In the interface, the method declaration
void op1 (Comp c); is created and in ClTestImpl.java an empty implementation
in created. I would like to put some code in this empty implementation and
somehow call this method in the generated GMF editor.

Unfortunately, Eugenia doesn't provide such a feature. As a matter of fact, Eugenia doesn't generate any code at all; it just produces the .gmfxxx models and then passes them on to GMF for the code generation step.